1. Since a MT won't downshift automatically if they have too tall of a top gear some buyers will be upset that they have to downshift for a hill or a pass and feel that the car is underpowered.

2. It's been mentioned previously in another thread that the EPA test for MT has set shift points. If a tall gear will give real world FE savings but cause the engine to perform in a way that requires the EPA tester to shift to a lower gear then the result could be a lower EPA score.